Inferring bacterial transmission dynamics using deep sequencing genomic surveillance data

Within host variation is increasingly being cited as a tool to distinguish transmission pairs. However, the role of within-host diversity in transmission is understudied due to a lack of experimental and clinical datasets that capture within-host diversity in both donors and recipients. Here, we assess the utility of deep-sequenced genomic surveillance within a mouse transmission model where the gastrointestinal pathogen Citrobacter rodentium was controllably spread during co-housing of infected and naïve animals. We observed that within 38 host variants were maintained over multiple transmission steps until fixation or elimination and present a model for inferring the likelihood that a given pair of samples are linked by transmission, by comparing the allelic frequency at variant genomic loci. Because within-host single nucleotide variants (iSNVs) can repeatedly pass from donor to recipient along the transmission chain, sharing of iSNVs offers limited discriminatory power in identifying a transmission pair. Beyond the presence and absence of within-host variants, we show that differences arising in the relative abundance of iSNVs (allelic frequency) can infer transmission pairs more precisely. However, in applying this method it is important to carefully consider routes of transmission, bottleneck sizes and mutation rates. Additionally, genomic artefacts must be carefully curated to avoid spurious inferences of transmission. An important component of our approach is that the inference is based solely on sequence data, without incorporating epidemiological or demographic data for context. Therefore, it can be adapted and used to complement existing epidemiologic tools

Molecular methods enhance the detection of pyoderma-related Streptococcus pyogenes and emm-type distribution in children.

BACKGROUND: Streptococcus pyogenes-related skin infections are increasingly implicated in the development of rheumatic heart disease (RHD) in lower-resourced settings, where they are often associated with scabies. The true prevalence of S. pyogenes-related pyoderma may be underestimated by bacterial culture. METHODS: A multiplex qPCR for S. pyogenes, Staphylococcus aureus and Sarcoptes scabiei was applied to 250 pyoderma swabs from a cross-sectional study of children <5 years in The Gambia. Direct PCR-based emm-typing was used to supplement previous whole genome sequencing (WGS) of cultured isolates. RESULTS: Pyoderma lesions with S. pyogenes increased from 51% (127/250) using culture to 80% (199/250) with qPCR. Compared to qPCR, the sensitivity of culture was 95.4% for S. pyogenes (95% CI 77.2-99.9) in samples with S. pyogenes alone (22/250, 9%), but 59.9% (95% CI 52.3-67.2) for samples with S. aureus co-infection (177/250, 71%). Direct PCR-based emm-typing was successful in 50% (46/92) of cases, identifying 27 emm-types, including six not identified by WGS (total 52 emm-types). CONCLUSIONS: Bacterial culture significantly underestimates the burden of S. pyogenes in pyoderma, particularly when co-infected with S. aureus. Molecular methods should be used to enhance the detection of S. pyogenes in surveillance studies and clinical trials of preventative measures in RHD-endemic settings

Hospital-based Surveillance for Pediatric Bacterial Meningitis in the Era of the 13-Valent Pneumococcal Conjugate Vaccine in Ghana.

BACKGROUND: Global surveillance for vaccine preventable invasive bacterial diseases has been set up by the World Health Organization to provide disease burden data to support decisions on introducing pneumococcal conjugate vaccine (PCV). We present data from 2010 to 2016 collected at the 2 sentinel sites in Ghana. METHODS: Data were collected from children <5 years of age presenting at the 2 major teaching hospitals with clinical signs of meningitis. Cerebrospinal fluid specimens were collected and tested first at the sentinel site laboratory with conventional microbiology methods and subsequently with molecular analysis, at the World Health Organization Regional Reference Laboratory housed at the Medical Research Council Unit The Gambia, for identification of Streptococcus pneumoniae, Haemophilus influenzae, and Neisseria meningitidis, the 3 most common bacteria causing meningitis. RESULTS: There were 4008 suspected cases of meningitis during the surveillance period, of which 31 (0.8%) were laboratory confirmed. Suspected meningitis cases decreased from 923 in 2010 to 219 in 2016. Of 3817 patients with available outcome data, 226 (5.9%) died. S. pneumoniae was the most common bacterial pathogen, accounting for 68.5% of confirmed cases (50 of 73). H. influenzae and N. meningitidis accounted for 6.8% (5 of 73) and 21.9% (16 of 73), respectively. The proportion of pneumococcal vaccine serotypes causing meningitis decreased from 81.3% (13 of 16) before the introduction of 13-valent PCV (2010-2012) to 40.0% (8 of 20) after its introduction (2013-2016). CONCLUSIONS: Cases of suspected meningitis decreased among children <5 years of age between 2010 and 2016, with declines in the proportion of vaccine-type pneumococcal meningitis after the introduction of 13-valent PCV in Ghana

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe

Maternal anemia is a potential risk factor for anemia in children aged 6-59 months in Southern Africa: a multilevel analysis

Background: The effect of maternal anemia on childhood hemoglobin status has received little attention. Thus, we examined the potential association between maternal anemia and childhood anemia (aged 6–59 months) from selected Southern Africa countries. Methods: A cross-sectional study using nationally representative samples of children aged 6–59 months from the 2010 Malawi, 2011 Mozambique, 2013 Namibia, and 2010–11 Zimbabwe demographic and health surveys (DHS) was conducted. Generalized linear mixed models (GLMMs) were constructed to test the associations between maternal anemia and childhood anemia, controlling for individual and community sociodemographic covariates. Results: The GLMMs showed that anemic mothers had increased odds of having an anemic child in all four countries; adjusted odds ratio (aOR = 1.69 and 95% confidence interval [CI]:1.37–2.13) in Malawi, (aOR = 1.71; 95% CI: 1.37–2.13) in Mozambique, (aOR = 1.55; 95% CI: 1.08–2.22) in Namibia, and (aOR = 1.52; 95% CI: 1.25–1.84) in Zimbabwe. Furthermore, the odds of having an anemic child was higher in communities with a low percentage of anemic mothers (aOR = 1.52; 95% CI: 1.19–1.94) in Mozambique. Conclusions: Despite the long-standing efforts to combat childhood anemia, the burden of this condition is still rampant and remains a significant problem in Southern Africa. Thus, public health strategies aimed at reducing childhood anemia should focus more on addressing infections, and micronutrient deficiencies both at individual and community levels in Southern Africa

Maternal overweight and obesity and the risk of caesarean birth in Malawi

Abstract Background Overweight and obese women are at risk of pregnancy and delivery complications. This study investigates the trend and association between maternal overweight and obesity on caesarean births in Malawi. Methods We utilised cross-sectional population-based Demographic Health Surveys (DHSs) data collected from mothers aged 18–49 years in 2004/05, 2010, and 2015/16 in Malawi. The outcome measure was caesarian birth within 5 years preceding the surveys. The main independent variable was maternal Body Mass Index (BMI) measured as weight in kilograms by height in meters squared (kg/m2) and categorized according to the World Health Organization (WHO) guidelines. Generalized estimating equations (GEE) regression models were constructed to analyze total samples of 6795, 4474 and 4363 in 2004/05, 2010 and 2015/16 respectively. Results There was an observed increase in the trend of caesarean births as well as maternal overweight and obesity from 2004 to 2015. The results of the multivariate analyses showed that maternal overweight (adjusted odds ratio [aOR] = 1.35; 95% Confidence Interval [CI] 1.01–1.83) in 2015/16 and (aOR = 1.36; 95% CI: 1.10–1.65) from 2004 to 2015 were risk factors for caesarean births in Malawi. In addition, being obese (aOR = 2.15; 95% CI: 1.12–4.11) in 2004/05, (aOR = 1.66; 95% CI: 1.08–2.55) in 2010, (aOR = 2.18; 95% CI: 1.48–3.21) in 2015/16, and (aOR = 2.16; 95% CI: 1.65–2.84) from 2004 to 2015) increased the risk of caesarean births. In addition, women who had one parity, and lived in the northern region were significantly more likely to have undergone caesarean birth. Conclusions In order to reduce non-elective cesarean birth in Malawi, specific public health programs should be focus on reducing overweight and obesity among women of reproductive age. More focus attention may be given to women with one parity, particularly in the urban and the northern region of Malawi

Predictors of exclusive breastfeeding knowledge and intention to or practice of exclusive breastfeeding among antenatal and postnatal women receiving routine care: a cross-sectional study

Abstract Background Despite consistent evidence showing the importance of exclusive breastfeeding (EBF) for six months, it remains a sub-optimal practice in The Gambia. This study aimed at investigating the determinants of EBF knowledge and intention to or practice of EBF. Methods A cross-sectional study was conducted among 334 women receiving care at the Edward Francis Small Teaching Hospital (EFSTH) from December 2015 to February 2016. Using a structured interviewer-administered questionnaire, knowledge on EBF was determined and scored. Participants scoring above or equal to the median were determined to have sufficient EBF knowledge. Multivariate logistic regression analyses were used to identify predictors of EBF knowledge and intention to or practice of exclusive breastfeeding. Results The proportion of women with sufficient exclusive breastfeeding knowledge and intended to or practice EBF were 60.2% and 38.6% respectively, while only 34.4% received EBF counseling. Earning ≥1500 GMD monthly (Adjusted Odds Ratio [aOR] 1.98; 95% Confidence Interval [Cl] 1.24, 3.16), having positive attitude (aOR 2.40; 95% Cl 1.40, 4.10) and partner supporting EBF (aOR 2.18; 95% Cl 1.23, 3.87) predicted sufficient EBF knowledge. Mothers aged 26–34 years (aOR 0.50; 9 5% Cl 0.31, 0.82) and EBF counseling (aOR 2.68; 95% Cl 1.68, 4.29) significantly associated with intention to or practice of exclusive breastfeeding. Conclusion In conclusion, improving EBF rates will, therefore, require improved access to information on EBF targeting low socio-economically disadvantaged and older mothers. In addition, emphasis on strengthening the ongoing EBF counseling already within the health system is required

Learning styles proffered by medical students in The Gambia

18 p.Introduction: In the last three decades, the proposition that students learn by following different styles has become a prominent topic in pedagogy worldwide. In The Gambia, learning styles in medical students are not known. Objective: To characterize the learning styles preferred by the students of the School of Medicine and Allied Health Sciences of The Gambia. Methods: A cross-sectional design was applied using the standardized VARK questionnaire for data collection, the analysis of which was performed using the SPSS software. Results: Most students preferred multimodal variants of learning; the bimodal variant was chosen more frequently. No significant associations were obtained between VARK scores and the sex or age of the students (p>0.05). Significant differences were reached for kinesthetic scores between preclinical and clinical students (p=0.031). In addition, a significant association was achieved in relation to the preferred unimodal variants among preclinical and clinical students. No significant differences were found regarding academic performance among students with unimodal or multimodal preferences (p>0.05). Conclusions: The application of the VARK questionnaire allowed the identification of preferred learning styles for particular ways of presenting information among medical students in The Gambia. Learning styles differed among students, most of whom had a preference for multimodal styles, which included the kinesthetic variant. These findings could be used to improve the quality of teaching.Introducción: En las últimas tres décadas, la proposición de que los estudiantes aprenden siguiendo diferentes estilos se ha convertido en un prominente tema en pedagogía a nivel mundial. En La Gambia no se conoce cuáles son los estilos de aprendizaje en estudiantes de Medicina. Objetivo: Caracterizar los estilos de aprendizaje de preferencia en estudiantes de la Escuela de Medicina y Ciencias Afines de la Salud en La Gambia. Métodos: Se aplicó un diseño transversal mediante el cuestionario estandarizado VARK para la recolección de datos, cuyo análisis se realizó con el uso del software SPSS. Resultados: La mayoría de los estudiantes prefirieron variantes multimodales de aprendizaje; la variante bimodal se escogió con más frecuencia. No se obtuvieron asociaciones significativas entre las puntuaciones VARK y el sexo o la edad de los estudiantes (p > 0,05). Se alcanzaron diferencias significativas para las puntuacioneskinestésicas entre estudiantes de preclínica y clínica (p = 0,031). Además, se logró una asociación significativa con relación a las variantes unimodales preferidas entre los estudiantes de preclínica y clínica. No fueron encontradas diferencias significativas en cuanto al rendimiento académico entre estudiantes con preferencias unimodales o multimodales (p > 0,05). Conclusiones: La aplicación del cuestionario VARK permitió la identificación de los estilos preferidos de aprendizaje para modos particulares de presentación de la información en estudiantes de Medicina en La Gambia. Los estilos de aprendizaje difirieron entre los estudiantes, la mayoría de los cuales tuvieron preferencia por los estilos multimodales, que incluían la variante kinestésica. Estos hallazgos pudieran emplearse para mejorar la calidad de la enseñanza

Additional file 1: of Maternal anemia is a potential risk factor for anemia in children aged 6–59 months in Southern Africa: a multilevel analysis

VIF and Tolerance for the four selected Southern African countries. Table S1 shows the multicollinearity using VIF and Tolerance for the four selected Southern African countries. (DOC 72 kb